Argumentation to Represent and Reason over Biological Systems

Adam Wyner, Luke Riley, Robert Hoehndorf, Samuel Croset

Research output: Chapter in Book/Report/Conference proceedingConference Proceeding (Non-Journal item)


In systems biology, networks represent components of biological systems and their interactions. It is a challenge to efficiently represent, integrate and analyse the wealth of information that is now being created in biology, where issues concerning consistency arise. As well, the information offers novel methods to explain and explore biological phenomena. To represent and reason with inconsistency as well as provide explanation, we represent a fragment of a biological system and its interactions in terms of a computational model of argument and argumentation schemes. Process pathways are represented in terms of an argumentation scheme, then abstracted into a computational model for evaluation, yielding sets of 'consistent' arguments that represent compatible biological processes. From the arguments, we can extract the corresponding processes. We show how the analysis supports explanation and systematic exploration in a biology network.
Original languageEnglish
Title of host publicationInformation Technology in Bio- and Medical Informatics
Subtitle of host publicationThird International Conference, ITBAM 2012, Vienna, Austria, September 4-5, 2012, Proceedings
EditorsChristian Böhm, Sami Khuri, Lenka Lhotská, M. Elena Renda
PublisherSpringer Nature
ISBN (Print)3642323944, 978-3642323942
Publication statusPublished - 01 Sept 2012


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